Analysis of reaction network systems using tropical geometry

DOI10.1007/978-3-319-24021-3_31MaRDI QIDQ3454561zbMATH OpenOpenAlexFDO

Authors Satya Swarup Samal, Holger Fröhlich, Ovidiu Radulescu, Dima Grigoriev

Publication date 25 November 2015

Published in Computer Algebra in Scientific Computing (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1508.05717

Mathematics Subject Classification ID

Nonlinear ordinary differential equations and systems (34A34) Nonnumerical algorithms (68W05) Biochemistry, molecular biology (92C40)

Abstract: We discuss a novel analysis method for reaction network systems with polynomial or rational rate functions. This method is based on computing tropical equilibrations defined by the equality of at least two dominant monomials of opposite signs in the differential equations of each dynamic variable. In algebraic geometry, the tropical equilibration problem is tantamount to finding tropical prevarieties, that are finite intersections of tropical hypersurfaces. Tropical equilibrations with the same set of dominant monomials define a branch or equivalence class. Minimal branches are particularly interesting as they describe the simplest states of the reaction network. We provide a method to compute the number of minimal branches and to find representative tropical equilibrations for each branch.

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Cited in

(14)

• Classical quasi-steady state reduction -- a mathematical characterization
• Algorithmic reduction of biological networks with multiple time scales
• Qualitative dynamics of chemical reaction networks: an investigation using partial tropical equilibrations
• Singular perturbations and scaling
• Tropicalization and tropical equilibration of chemical reactions
• Biochemical reaction networks: An invitation for algebraic geometers
• Model reduction of biochemical reactions networks by tropical analysis methods
• Vector-Space Methods and Kirchhoff Graphs for Reaction Networks
• A geometric method for model reduction of biochemical networks with polynomial rate functions
• scientific article; zbMATH DE number 7774177 (Why is no real title available?)
• Reduction of Chemical Reaction Networks with Approximate Conservation Laws
• The Disguised Toric Locus and Affine Equivalence of Reaction Networks
• Tropicalization of planar polynomial ODEs
• Parametric toricity of steady state varieties of reaction networks

Describes a project that uses

Uses Software

• polymake
• PoCaB
• BioModels
• z3

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